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Affymetrix Releases Axiom Genome-Wide Pan-African Array

Published: Friday, October 21, 2011
Last Updated: Friday, October 21, 2011
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The highest genomic coverage of African and African American genomes for disease association studies.

Affymetrix®, Inc. has announced at the ICHG/ASHG annual conference in Montreal, the worldwide launch of the Axiom® Genome-Wide Pan-African Array, the first commercial product to maximize genomic coverage of both common and rare alleles in populations of African ancestry, including West African, East African, and African American.

The Axiom Solution is the only microarray family of products to provide a complete set of population-optimized arrays for all three HapMap populations: Western European (CEU), East Asian (ASI), and Yoruba (YRI).

Each array is strategically designed to address the unique haplotype structure of these populations to ensure high genomic coverage and statistical power.

“We are currently using the Axiom Pan-African Array for prostate cancer, sickle-cell disease, and drug response research. With greater access to rare variants and increased coverage, I hope to gain better insights into new disease mechanisms.”

“The poor genomic coverage of currently available commercial arrays in African populations has significantly impacted our ability to understand the genetic factors that underlie the increased risk of African Americans for diseases such as cancer (prostate, breast, and colon) and cardiovascular and pulmonary disorders,” said Dr. Rick Kittles, Associate Professor of Medicine and Director of the Institute of Human Genetics at the University of Illinois at Chicago.

Dr. Kittles continued, “We are currently using the Axiom Pan-African Array for prostate cancer, sickle-cell disease, and drug response research. With greater access to rare variants and increased coverage, I hope to gain better insights into new disease mechanisms.”

“The marked improvement in genomic coverage of the Axiom Array is of enormous utility in our attempts to link genetic information and the delivery of personalized medicine,” said Dr. Joe G.N. Garcia, Earl M. Bane Professor of Medicine and Vice President for Health Affairs at the University of Illinois.

Dr. Garcia continued, “We anticipate that information derived from the discovery of important variants which modify risk, modulate responses to therapy, and drive the severity of disease in susceptible populations will be rapidly utilized within the University of Illinois Hospital and Health Sciences System to reduce health disparities.

Until now, studies of African American and African populations have been underrepresented in disease association studies because commercially available arrays of these populations were not optimized for the complex haplotype patterns of African genomes.

The Axiom Pan-African Array offers ~ 90 percent coverage of YRI alleles with minor allele frequency (MAF) ≥2.0 percent. In addition, it has been extensively validated in four African populations from the HapMap collection, including the Luhya from western Kenya (LWK), Maasai from eastern Kenya (MWK), Yoruba from Ibadan, Nigeria, and the African Ancestry in the Southwest USA (ASW).

In all cases, the Axiom Pan-African Array offers an incremental increase of 15-20 percent genomic coverage compared to other commercial arrays.

“African populations have a greater number of smaller haplotype blocks and singletons than European populations and thus require a more sophisticated array design strategy to achieve genomic coverage comparable to levels provided for European populations,” said Andy Last, Executive Vice President and Chief Commercial Officer at Affymetrix.

Last continued, “With the Axiom platform we have an unmatched capability to deliver population-optimized genotyping arrays to ensure that clinical researchers have specialized and cost effective tools to better investigate genetic susceptibility and health disparities in understudied populations.”

The Axiom Pan-African Array was designed by leveraging over 11 million common and rare genomic markers within the Axiom Genomic Database, the industry's largest supply of validated genomic markers.

The array contains more than 2.2 million informative markers that are proven to be heterozygous in the African genome, thus maximizing the analysis of each sample.

Compared to competing arrays with a similar number of markers, it has the highest coverage of variants in important biological categories such as the National Human Genome Research Institute (NHGRI), Catalog of Published Genome-Wide Association Studies, Sanger Cancer Genome Census genes, Major Histocompatibilty Complex (MHC) genes, cardiovascular genes, and immune and inflammation pathway genes. The array also offers coverage across chromosomes X and Y, the mitochondrial genome, and drug metabolism genes.

The complete Axiom Genotyping Solution consists of Axiom Genome-Wide Pan-African Array Plates, the new Axiom 2.0 Reagent Kits, and the new Genotyping Console 4.1 for automated allele calling and quality control.

The Axiom Array Plates are used on the automated target preparation station and GeneTitan® Instrument for hands-free processing.

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